# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1fsoA 139 9.86e-03 1rhoA b.1.18.8 60007 1rhoA 145 1.17e-02 1rhoA b.1.18.8 21899 1jh5A 144 1.54e-02 b.22.1.1 66697 1kmtA 141 2.09e-02 b.1.18.8 77442 1rhoC 145 4.99e-02 1rhoA b.1.18.8 21901 1nepA 130 5.79e-02 b.1.18.7 80440 1kxgA 152 9.35e-02 b.22.1.1 73145 1ajw 145 3.01e-01 1rhoA b.1.18.8 21905 1rwiA 270 6.16e-01 unknown_sccs -4603 1kjvB 100 7.37e-01 b.1.1.2 77423 6rxn 46 7.87e-01 1rb9 g.41.5.1 45222 1el6A 219 8.08e-01 1el6B d.182.1.1 42606 1uxzA 131 8.45e-01 b.18.1.10 -3110 1bkb 136 9.35e-01 1bkb b.34.5.2 24609 b.40.4.5 25341 1el6B 219 9.84e-01 1el6B d.182.1.1 42607 1eal 127 1.24e+00 1hmt b.60.1.2 27227 1fngA 192 1.31e+00 1iakA b.1.1.2 59904 d.19.1.1 59905 1fneA 192 1.34e+00 1iakA b.1.1.2 59896 d.19.1.1 59897 1lurA 339 1.76e+00 b.30.5.4 84717 1iz6A 138 1.91e+00 b.34.5.2 76976 b.40.4.5 76977 1gr3A 160 1.96e+00 b.22.1.1 65476 1jqiA 388 2.18e+00 a.29.3.1 67087 e.6.1.1 67088 1dg6A 191 2.20e+00 1d4vB b.22.1.1 23883 1ehkB 168 2.21e+00 2cuaA b.6.1.2 23041 f.17.2.1 43625 1n7eA 97 2.41e+00 b.36.1.1 -3745 1ieaA 192 2.53e+00 1iakA b.1.1.2 21631 d.19.1.1 38205 1rj8A 164 2.98e+00 b.22.1.1 -3263 1ixmA 192 3.10e+00 1ixmA d.123.1.1 41114 1tit 98 3.13e+00 1tit b.1.1.4 21716 1go3E 187 3.17e+00 b.40.4.5 83054 d.230.1.1 83055 1bvp1 349 3.27e+00 1bvp1 1g9oA 91 3.58e+00 1pdr b.36.1.1 60400 1kcvL 214 3.58e+00 b.1.1.1 72317 b.1.1.2 72318 2cuaA 135 3.59e+00 2cuaA b.6.1.2 23039 1g7pB 99 3.73e+00 b.1.1.2 70155 1tgoA 773 3.84e+00 1tgoA c.55.3.5 33721 e.8.1.1 43010 1tzaA 134 3.86e+00 1q3oA 109 3.96e+00 b.36.1.1 -3776 1cx4A 305 3.99e+00 b.82.3.2 59099 b.82.3.2 59100 1ahsA 126 4.08e+00 1ahsA b.19.1.1 23794 1ixmB 192 4.36e+00 1ixmA d.123.1.1 41115 1qfhA 212 4.37e+00 1qfhA b.1.18.10 21893 b.1.18.10 21894 1g3gA 164 4.50e+00 1g6gA b.26.1.2 23918 1aozA 552 4.54e+00 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1d2qA 173 5.08e+00 1d4vB b.22.1.1 23894 1ds6B 180 5.23e+00 1rhoA b.1.18.8 21898 1gxuA 91 5.51e+00 d.58.10.1 76378 8fabA 212 5.52e+00 8fabA b.1.1.1 19772 b.1.1.2 20882 1hdmA 201 5.52e+00 1iakA b.1.1.2 21583 d.19.1.1 38157 1mz5A 638 5.86e+00 b.29.1.15 79679 b.68.1.1 79680 1v7wA 807 5.91e+00 1i4fB 100 6.04e+00 1agdB b.1.1.2 61689 1bv1 159 6.18e+00 1bv1 d.129.3.1 41313 1lk2B 99 6.24e+00 b.1.1.2 -2576 1fzkB 99 6.50e+00 1agdB b.1.1.2 60151 1n08A 163 6.54e+00 b.43.5.1 79730 1agdB 99 6.63e+00 1agdB b.1.1.2 20742 1mhcB 99 6.69e+00 1agdB b.1.1.2 20832 1hsbB 99 6.82e+00 1agdB b.1.1.2 20737 1duzB 100 6.82e+00 1agdB b.1.1.2 20671 1mm4A 170 6.87e+00 f.4.1.2 79294 1fzoB 99 6.87e+00 1agdB b.1.1.2 60157 1g6gA 127 6.98e+00 1g6gA b.26.1.2 23916 1dcs 311 7.02e+00 1dcs b.82.2.1 28124 1k5nB 100 7.09e+00 b.1.1.2 77268 1glv 303 7.17e+00 1gsa c.30.1.3 31721 d.142.1.1 41480 1hxmA 229 7.23e+00 1hxmA b.1.1.1 61367 b.1.1.2 61368 1pk6C 129 7.28e+00 b.22.1.1 -3293 1nkoA 132 7.41e+00 b.1.1.1 85829 1usuA 260 7.60e+00 unknown_sccs -9045 1a49A 530 7.70e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1kpuB 99 7.94e+00 b.1.1.2 84458 1n1tA 641 8.25e+00 b.29.1.15 79821 b.68.1.1 79822 1qhtA 775 8.55e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1difA 99 8.56e+00 1fmb b.50.1.1 26503 1i92A 91 8.91e+00 1pdr b.36.1.1 61990 1c3hA 137 9.11e+00 b.22.1.1 -3255 1oq1A 223 9.26e+00 unknown_sccs -3455 1l6oA 95 9.63e+00 b.36.1.1 84534 1pk6A 133 9.69e+00 b.22.1.1 -3287 1mfgA 95 9.72e+00 b.36.1.1 79043 1obpA 159 9.76e+00 1obpA b.60.1.1 27092 1suh 146 1.00e+01 1edhA b.1.6.1 22206 1lci 550 1.03e+01 1lci e.23.1.1 43349 1ne6A 283 1.04e+01 b.82.3.2 -4918 b.82.3.2 -4919 1kzkA 99 1.06e+01 b.50.1.1 73371 1d8cA 723 1.06e+01 1d8cA c.1.13.1 29325 1i88A 389 1.08e+01 c.95.1.2 66070 c.95.1.2 66071 1n99A 166 1.11e+01 b.36.1.1 85459 b.36.1.1 85460 1cqkA 101 1.14e+01 1cqkA b.1.1.2 21547 3fivA 116 1.14e+01 1fmb b.50.1.1 26768 1jj2P 95 1.17e+01 1ffkN b.34.5.1 63101 1s72Q 96 1.18e+01 1nh0A 99 1.22e+01 b.50.1.1 -4299 1ox0A 430 1.26e+01 c.95.1.1 87495 c.95.1.1 87496 1cs6A 382 1.26e+01 1cs6A b.1.1.4 21760 b.1.1.4 21761 b.1.1.4 21762 b.1.1.4 21763 4fiv 113 1.29e+01 1fmb b.50.1.1 26762 2fivA 116 1.30e+01 1fmb b.50.1.1 26766 1bfeA 119 1.34e+01 1pdr b.36.1.1 24775 1o22A 170 1.34e+01 d.238.1.1 86557 1lfo 128 1.36e+01 1hmt b.60.1.2 27223 1nteA 82 1.43e+01 b.36.1.1 86163 1d4vB 163 1.45e+01 1d4vB b.22.1.1 23884 1r6jA 82 1.47e+01 b.36.1.1 -3732 1hdmB 193 1.53e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1flmA 122 1.53e+01 1axj b.45.1.1 25747 1pkn 530 1.54e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1ois 223 1.56e+01 1a36A e.15.1.1 43267 1qqsA 174 1.58e+01 1nglA b.60.1.1 27143 1edhA 226 1.64e+01 1edhA b.1.6.1 22198 b.1.6.1 22199 1o4yA 288 1.76e+01 b.29.1.2 -3404 1rr9A 200 1.79e+01 unknown_sccs -9100 1cwvA 492 1.81e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1b6fA 159 1.83e+01 1bv1 d.129.3.1 41316 1ms9A 648 1.87e+01 b.29.1.15 85088 b.68.1.1 85089 3ladA 476 1.87e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1mo1A 87 1.89e+01 d.94.1.1 -10640 1fivA 113 1.89e+01 1fmb b.50.1.1 26764 1dfx 125 1.89e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1i05A 180 1.90e+01 1mup b.60.1.1 27130 1ewfA 456 1.92e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1pmi 440 1.93e+01 1pmi b.82.1.3 28114 1p7tA 731 1.94e+01 c.1.13.1 -5600 1eb7A 323 1.94e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1b5eA 246 1.95e+01 1b5eA d.117.1.1 41056 1o91A 178 1.95e+01 b.22.1.1 -3282 1h9oA 112 2.00e+01 1qadA d.93.1.1 60837 1ok8A 394 2.01e+01 b.1.18.4 -2737 f.10.1.1 -12384 1iqaA 160 2.02e+01 b.22.1.1 71274 1qsvA 101 2.02e+01 1fltX b.1.1.4 21771 1aszB 490 2.10e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1fm4A 159 2.11e+01 1bv1 d.129.3.1 76186 1p32A 209 2.20e+01 1p32A d.25.1.1 38379 1cgt 684 2.21e+01 1cxlA b.1.18.2 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1idaA 99 2.23e+01 1fmb b.50.1.1 26715 1jqpA 438 2.24e+01 b.61.5.1 77162 d.3.1.1 77163 1o7iA 119 2.25e+01 b.40.4.3 86642 1hvc 203 2.26e+01 1hvc b.50.1.1 26614 1nciA 110 2.30e+01 1edhA b.1.6.1 22191 1be9A 119 2.32e+01 1pdr b.36.1.1 24774 2pcfB 250 2.32e+01 1hcz i.4.1.1 45911 1axj 122 2.33e+01 1axj b.45.1.1 25749 1jpyB 137 2.33e+01 g.17.1.6 67066 1liuA 528 2.33e+01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1mqoA 227 2.34e+01 1ld4A 264 2.40e+01 i.6.1.1 77886 1h91A 180 2.41e+01 b.60.1.1 60805 1rreA 200 2.43e+01 unknown_sccs -9106 1ehxA 94 2.48e+01 1ehxA b.1.18.13 21950 1i8kA 107 2.49e+01 b.1.1.1 71130 1gu3A 149 2.52e+01 b.18.1.14 76350 1g1cA 99 2.53e+01 b.1.1.4 65078 5hvpA 99 2.53e+01 1fmb b.50.1.1 26605 1df3A 162 2.54e+01 1mup b.60.1.1 27134 1kapP 479 2.59e+01 1sat unknown_sccs 28012 d.92.1.6 40298 1sftA 388 2.61e+01 1bd0A b.49.2.2 26482 c.1.6.1 28644 1gt1A 159 2.61e+01 b.60.1.1 -4436 1svpA 161 2.61e+01 1svpA b.47.1.3 26384 1dazC 99 2.66e+01 1hvc b.50.1.1 26501 1ewcA 214 2.72e+01 3seb b.40.2.2 25199 d.15.6.1 37788 1hn2A 159 2.77e+01 b.60.1.1 65890 1dxrH 258 2.80e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 1oruA 195 2.81e+01 unknown_sccs -4390 1jv4A 162 2.82e+01 b.60.1.1 67343 1fw1A 216 2.84e+01 a.45.1.1 60051 c.47.1.5 60052 1o6sB 105 2.86e+01 b.1.6.1 81096 1bbpA 173 2.86e+01 1bbpA b.60.1.1 27147 6prcH 258 2.87e+01 6prcH b.41.1.1 25457 f.23.10.1 43436 1icfA 175 2.88e+01 1cs8A d.3.1.1 37067 1sr9A 644 2.89e+01 1qauA 112 2.89e+01 1qauA b.36.1.1 24779 1v5sA 126 2.89e+01 1nkgA 508 3.01e+01 1f97A 212 3.01e+01 1f97A b.1.1.1 19763 b.1.1.4 21764 1qynA 153 3.04e+01 d.33.1.1 -9585 1nfiC 301 3.06e+01 b.1.18.1 21943 b.2.5.3 22456 1nh1A 330 3.11e+01 unknown_sccs -11798 1qunB 279 3.13e+01 b.2.3.2 22411 b.2.3.2 22412 1mup 166 3.13e+01 1mup b.60.1.1 27133 2apr 325 3.13e+01 2er7E b.50.1.2 26819 1hcz 252 3.16e+01 1hcz b.2.6.1 22464 b.84.2.2 28250 3aprE 325 3.24e+01 2er7E b.50.1.2 26820 1i82A 189 3.28e+01 1i82A b.1.9.2 61937 1qmrA 159 3.28e+01 1bv1 d.129.3.1 41314 1ncg 110 3.29e+01 1edhA b.1.6.1 22193 1gmmA 133 3.29e+01 b.18.1.10 65314 1kb5B 117 3.29e+01 1kb5B b.1.1.1 20632 1rb9 53 3.31e+01 1rb9 g.41.5.1 45214 1ia9A 280 3.32e+01 1ia9A d.144.1.5 62113 1o7sA 127 3.34e+01 b.1.1.1 86644 1iv8A 720 3.37e+01 b.71.1.1 76842 c.1.8.1 76843 1q7rA 219 3.37e+01 c.23.16.1 -6507 1b2pA 119 3.40e+01 1b2pA b.78.1.1 27998 1b4vA 504 3.40e+01 1b8sA c.3.1.2 30334 d.16.1.1 37865 1jzuA 157 3.42e+01 b.60.1.1 84271 1n7fA 97 3.43e+01 b.36.1.1 -3746 1n4wA 504 3.43e+01 c.3.1.2 -5991 d.16.1.1 -9209 1dx8A 70 3.44e+01 1rb9 g.41.5.1 45243 1xgsA 295 3.44e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1knlA 130 3.46e+01 b.42.2.1 72780 1tljA 213 3.47e+01 1qtqA 553 3.47e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1i06A 180 3.49e+01 1mup b.60.1.1 27131 1v04A 355 3.49e+01 unknown_sccs -4592 1iicA 422 3.49e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1b8sA 504 3.49e+01 1b8sA c.3.1.2 30335 d.16.1.1 37866 8rxnA 52 3.51e+01 1rb9 g.41.5.1 45215 1fltY 95 3.56e+01 1fltX b.1.1.4 21766 1p5vA 235 3.58e+01 b.1.11.1 87812 b.7.2.1 87813 1l3aA 228 3.61e+01 d.18.1.2 73531 1n0uA 842 3.62e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1otcA 495 3.64e+01 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1pdr 99 3.65e+01 1pdr b.36.1.1 24771 1ewqA 765 3.67e+01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1v7oA 165 3.69e+01 unknown_sccs -10249 1lxnA 99 3.70e+01 d.58.48.1 84737 1sqjA 789 3.72e+01 1mxtA 504 3.76e+01 c.3.1.2 79671 d.16.1.1 79672 1n1pA 504 3.76e+01 c.3.1.2 -5988 d.16.1.1 -9206 1qttA 117 3.76e+01 1a1x b.63.1.1 27516 1kit 757 3.81e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1ijhA 504 3.81e+01 c.3.1.2 66161 d.16.1.1 66162 1knmA 130 3.81e+01 b.42.2.1 72781 1i8aA 189 3.85e+01 1i82A b.1.9.2 61951 1nfiA 301 3.90e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1gthA 1025 3.96e+01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1omwA 689 3.97e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1qfxA 460 3.98e+01 1qfxA c.60.1.2 33994